505 Works

Mrtrix3 iFOD2 ROI Tracking (dwi)

Brad Caron
This app will generate multiple ROI to ROI tractograms using mrtrix3's probabilistic iFOD2 algorithm and anatomically constrained tractography framework (ACT).

combineROI

Sophia Vinci-Booher
This app will combine two ROI datatype datasets into one ROI datatype dataset. If, for example, there are 3 rois in the first ROI dataset and 2 rois in the second ROI dataset, the output ROI data set will contain 5 rois. NOTE: This app can be used to extract one roi from an ROI dataset. If you enter the same roi in the roi1 and roi2 fields, the resulting ROI will simply be that...

Trekker ROI Tracking (dwi) - v1.0

Brad Caron
Brainlife App (wrapper) for dMRI based fiber tracking between ROIs using parallel transport tractography

Intersect Tracts with ROI

Brad Caron
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ROI to ROI Tracking - MRTrix 0.2.12

Ilaria Sani, Soichi Hayashi, Franco Pestilli & Brad Caron
This app will perform tracking between 2 cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. Inputs include: parcellation (freesurfer; atlas optional) with ROI niftis (generated from app-roiGeneration), dt6 from dtiinit, and ROI pairings. Outputs include a track.tck for each pairing of ROIs, a classification structure, and a fg_classified structure which can then be fed into other apps on the website (example: Clean WMC Output).

Laplace Beltrami Spectrum: Eigenvalues Only

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum using matlab

FreeSurfer Postprocessing

Brent McPherson
The converts labeled volumes to .nii.gz, creates white matter and corpus callosum masks, performs alignment to MNI space, and creates a 278 cortical labeled volume from Shen et al. 2013.

HD-BET

Anibal Solon Heinsfeld
HD-BET is an automated brain extraction method for MRI using neural networks.

fMRIPrep - Volume Output

Daniel Levitas, David Hunt, Josh Faskowitz & Soichi Hayashi
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

Linearly align DWI to another DWI with FSL Flirt

Brad Caron
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Independent evaluation of the reliability of major human white matter tracts mapped via brainlife.io

Franco Pestilli, Jan Kurzawski & Kyriaki Mikellidou
Test data

Independent evaluation of the reliability of major human white matter tracts mapped via brainlife.io

Franco Pestilli, Jan Kurzawski & Kyriaki Mikellidou
Retest data

dsi-studio-tt2trk

Convert TRK format to TinyTrack format

Extract summary statistics of diffusion measures mapped to cortical surface inside tract endpoints

Brad Caron
This app will compute multiple summary statistics from measures mapped to the cortical midthickness surface on a per-endpoint ROI basis. This app takes in a cortexmap datatype and an optional parcellation/surface datatype. This app will compute the following summary statistics: minimum, maximum, mean, median, mode, standard deviation, and nonzero vertex count. The app will output a csv for each summary measure summarizing the diffusion measures in each endpoint ROI. These csvs can be used for...

Extract_files

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Generate ROIs from pRF Eccentricity Estimates

Brad Caron
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Network Report

App to generate reports from networks. This includes network properties, node attributes and their respective distributions.

Justin Reslice T1w App

Justin Kilmarx
This is a template for a python-based brainlife.io/app

CIT168 parcellation of human subcortical brain nuclei

Daniel Bullock & Soichi Hayashi
A dockerized parcellation of human subcortical brain nuclei from the work of Pauli et al. 2018

Freesurfer Statistics

Brad Caron
This app will convert important parcellation statistics, including volume, thickness, and curvature, to a .csv file for each hemisphere. These can be used for group analyses.

Freesurfer

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Freesurfer segments the t1w anatomical data into functionally different parts of the brain. Segmentation/parcellation can then be fed to many other subsequent analysis.

Tract Analysis Profiles (NODDI)

Brad Caron
Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA

Multi-Atlas Transfer Tool - old (w/surface output)

Soichi Hayashi, Josh Faskowitz, Franco Pestilli, Brent McPherson & Brad Caron
brainlife.io version of multi atlas transfer tools (maTT). Specifically, this is an implemenation of maTT2, which uses the gcs files trained on the mindboggle-101 data. The GCS files are automatically pulled from the maTT fishare directory if not present locally. Inputs include: freesurfer, t1, atlas. Outputs include: parc.nii.gz (for each atlas indicated) & remapped LUT text file (for each atlas indicated). These outputs are in the space of the T1w that was submitted to FreeSurfer's...

Matlab example

Example template for network template using matlab

Tract Analysis Profiles - Dipy

Brad Caron
Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA

Registration Year

  • 2021
    22
  • 2020
    205
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    504
  • Service
    1

Affiliations

  • The University of Texas at Austin
    4
  • Indiana University
    4